Abstract. A 1-D model system, consisting of the 1-D version of the Princeton Ocean Model (POM) coupled with the European Regional Seas Ecosystem Model (ERSEM) has been applied to a sub-basin of the Baltic Proper, the Bornholm basin. The model has been forced with 3h meteorological data for the period 1979-1990, producing a 12-year hindcast validated with datasets from the Baltic Environmental Database for the same period. The model results demonstrate the model to hindcast the time-evolution of the physical structure very well, confirming the view of the open Baltic water column as a three layer system of surface, intermediate and bottom waters. Comparative analyses of modelled hydrochemical components with respect to the independent data have shown that the long-term system behaviour of the model is within the observed ranges. Also primary production processes, deduced from oxygen (over)saturation are hindcast correctly over the entire period and the annual net primary production is within the observed range. The largest mismatch with observations is found in simulating the biogeochemistry of the Baltic intermediate waters. Modifications in the structure of the model (addition of fast-sinking detritus and polysaccharide dynamics) have shown that the nutrient dynamics are linked to the quality and dimensions of the organic matter produced in the euphotic zone, highlighting the importance of the residence time of the organic matter within the microbial foodweb in the intermediate waters. Experiments with different scenarios of riverine nutrient loads, assessed in the limits of a 1-D setup, have shown that the external input of organic matter makes the open Baltic model more heterotrophic. The characteristics of the inputs also drive the dynamics of nitrogen in the bottom layers leading either to nitrate accumulation (when the external sources are inorganic), or to coupled nitrification-denitrification (under strong organic inputs). The model indicates the permanent stratification to be the main feature of the system as regulator of carbon and nutrient budgets. The model predicts that most of the carbon produced in the euphotic zone is also consumed in the water column and this enhances the importance of heterotrophic benthic processes as final closure of carbon and nutrient cycles in the open Baltic.